Dienekes has just posted a paper studying the autosomal and mtDNA of some Mesolithic Iberians and the conclusion is that they were very different from Basque and southern Europeans in general and more like northern Europeans, supporting the commonly held idea that pre-farming DNA has mainly survived in the north. The mt DNA (U) is stated to be more evidence of the uniformity of pre-farming Europeans.

From an archaeological point of view, I find this believable. The main expansion post-LGM was in the Magdalenian culture which is now thought to be an intrusion from the east about 18000 years ago. They then spread out all over west, central and northern Europe in various guises. I suspect this uniformity is due to most hunter-gatherers having common roots about 20000 years back in the east meaning there was little deeper time east-west refuge contrast that contributed to modern DNA.

This is another blow to any notion that the Basques were in-situ descendants of an ice age western refuge. Most already thought this in terms of yDNA and now mtDNA and autosomal is strongly agreeing with this. It is of course a tiny sample.

Dienekes has just posted a paper studying the autosomal and mtDNA of some Mesolithic Iberians and the conclusion is that they were very different from Basque and southern Europeans in general and more like northern Europeans, supporting the commonly held idea that pre-farming DNA has mainly survived in the north. The mt DNA (U) is stated to be more evidence of the uniformity of pre-farming Europeans.

This is what the paper says:

Quote from: Sanchez-Quinto.et.al.2012

In the genomic analysis, it is interesting to see that the La Braña individuals do not cluster with modern populations from Southern Europe, including those from the Iberian Peninsula. The first PC separates a north-south distribution, whereas the second follows a general east-west pattern in modern Europeans. The position of La Braña individuals in the 1000 Genomes Project data and the 1KG Pomnichip PCAs suggests that the uniform Mesolithic substrate could be related to modern Northern European populations but may represent a gene pool that is no longer present in contemporary Southern European populations. In the latter PCA, where the origin of each Iberian sample is known, it is possible to see that the Mesolithic specimens are not related to modern Basques, contrary to what has been previously suggested in some recent studies [39].

Ancient genomics from Neolithic individuals from Scandinavia [18] supports that the spread of agriculture into Europe involved the expansion of populations from the Middle East that eventually assimilated the contemporaneous hunter gatherers. Modern European populations seem to derive essentially from those Neolithic migrants [18]. Until now, however, the genetic affinities of the Mesolithic populations to the modern Europeans were largely unknown. Our partial La Braña 1 and 2 genomic data show that modern Iberian populations are not descendants of the local hunter-gatherers inhabiting the same region prior to the arrival of farmers and thus support a genetic shift in that region between the Mesolithic and modern populations.

In figure-S2, one can see that the Mesolithic Individuals are Asian-shifted with respect to modern Europeans.

The in figure-S3, one can see that the Mesolithic Individuals cluster within NW Europeans, that is CEU and GBR, now Basques appear to be as distant from them as Finns are, so it is not a Northern vs. Southern European thing, but NW Europeans having the closest similarities and then Southern Europeans and Finns. Granted some Finns do cluster very close to the individuals, whereas the closest Iberian individual is not even a Basque, but someone from Valencia.

From an archaeological point of view, I find this believable. The main expansion post-LGM was in the Magdalenian culture which is now thought to be an intrusion from the east about 18000 years ago. They then spread out all over west, central and northern Europe in various guises. I suspect this uniformity is due to most hunter-gatherers having common roots about 20000 years back in the east meaning there was little deeper time east-west refuge contrast that contributed to modern DNA.

This could have some support on the fact that the two hunter-gatherers do seem to be Asian-shifted in Figure-S2. However, they are definitely post-Magdalenian, as their dating is 7000 ybp, clearly outside of the Magdalenian period.

This is another blow to any notion that the Basques were in-situ descendants of an ice age western refuge. Most already thought this in terms of yDNA and now mtDNA and autosomal is strongly agreeing with this. It is of course a tiny sample.

From the autosomal* point of view, yes, there is definitely some re-thinking to do, given that Basques aren’t any closer to these Mesolithic Iberians than other Iberians. From the yDNA point of view, well British guys who are majority R1b are the closest modern Europeans to these Mesolithic samples, from the mtDNA point of view, there is evidence that points to the presence of mt-DNA H in Magdalenian Cantabria, and mt-DNA H in Mesolithic Guipuzcoans.

*Now that I think of it, they said the following in the abstract

Quote from: Sanchez.Quinto.et.al.2012

Furthermore, analyses of 1.34% and 0.53% of their nuclear genomes, containing about 50,000 and 20,000 ancestry informative SNPs, respectively, show that these two Mesolithic individuals are not related to current populations from either the Iberian Peninsula or Southern Europe.

But in Figure-S3 we do find the Iberians to be closely related to the two folks:

As a whole they are indeed closer than Finns, although not as close as NW Europeans. Something else I noticed in PCA plot S3, is that Basque usually cluster in a certain location tightly relative to the other Iberians, however here they are scattered all over the place, this might be due to the smaller number of SNPs used to construct the plots.(50,000 and 20,000 SNPs respectively)

"Closest" doesn't necessarily mean "close". Dienekes commented, "So while they are more related to Northern than to Southern Europeans, they are well outside the range of modern European variation."

If you see my comment over at Dienekes, I said that one should expect for ancient samples to fall outside the range of modern European variation based on the time frame of drift. Modern Europeans have 7000 years of drifting from these ancient Europeans, and if you add to that the input of a West Asian population which probably was a lot more differentiated from those ancient HG, then you get that picture. Of course, Dienekes concludes that the input of West Asian farmers was heavy, but we really do not know how much of the drift is due to normal drift, and how much is due to modern Europeans receiving Neolithic DNA. I do agree that if they sequenced the y-DNA they ought to release the haplogroups soon.

Nope, they are male, I actually talked about those findings here a while back. Here is what the paper says:

Quote from: Sanchez.Quinto.et.al.2012

The generated data covered 41,320,020 nucleotide positions for La Braña 1 and 16,876,146 for La Braña 2; thus, about 1.34% and 0.53% of the La Bran˜ a 1 and 2 genomes were retrieved, respectively. The read average length was 74.7 and 59.5 nucleotides, respectively (Table S4), shorter than the 85.7 nucleotides observed in the mtDNA reads (Table S3) but similar to the length previously reported for DNA extracted from Neanderthal remains [30]. The ratio of X chromosome versus Y chromosome sequences was close to 9:1 (n = ~18,000 versus n = ~2,000 reads, and n = ~8,000 versus n = ~1,000 for La Braña 1 and 2, respectively), consistent with the length ratio between both sex chromosomes. This would confirm the previous anthropological identification of La Braña specimens as males.

I thought this part was also interesting:

Quote from: Sanchez.Quinto.et.al.2012

A worldwide genomic principal component analysis (PCA) with data from the 1000 Genomes Project [31] places La Braña 1 and 2 near, but not within the variation of current European populations (Figure S2). However, when compared exclusively to European populations, La Braña 1 and 2 fall closer to Northern European populations such as CEU and Great Britons than Southern European groups such as Iberians or Tuscans (Figure 3). With 1KGPomni chip [31] data, the PCA generates a similar pattern (Figure S3), although the general geographic structure is less clear because of the limited number of SNPs (see Supplemental Experimental Procedures).

I wonder why they did not report the y haplogroups of these two skeletons. Are they not confident enough in their findings?

Didn't get to read it yet. Maybe they are female?

I read the report quickly. Both skeletons are male.

Part of it is a little section called, "Genomic Contamination Estimates", although, not being a geneticist, I cannot swear I completely understood it. Here is what it says about y-dna:

Quote

Less numerous y chromosome heterogeneities in two or more reads (91 out of 21,203 nucleotides and 31 out of 8,567 for La Braña 1 and 2, respectively) yielded similar values (0.4% and 0.36%). These contamination figures are overestimates, because sequencing errors are likely included in the existing reads.

I found surprising the affirmation that "Modern European populations seem to derive essentially from those Neolithic migrants" and the footnote redirects to an article by Pontus Skoglund et alii. I don´t have the full article but the abstract says find that the farmer is genetically most similar to extant southern Europeans, contrasting sharply to the hunter-gatherers, whose distinct genetic signature is most similar to that of extant northern Europeans. Our results suggest that migration from southern Europe catalyzed the spread of agriculture and that admixture in the wake of this expansion eventually shaped the genomic landscape of modern-day Europe which is not the same, anyone read that article?

Dienekes has just posted a paper studying the autosomal and mtDNA of some Mesolithic Iberians and the conclusion is that they were very different from Basque and southern Europeans in general and more like northern Europeans, supporting the commonly held idea that pre-farming DNA has mainly survived in the north. The mt DNA (U) is stated to be more evidence of the uniformity of pre-farming Europeans.

This is what the paper says:

Quote from: Sanchez-Quinto.et.al.2012

In the genomic analysis, it is interesting to see that the La Braña individuals do not cluster with modern populations from Southern Europe, including those from the Iberian Peninsula. The first PC separates a north-south distribution, whereas the second follows a general east-west pattern in modern Europeans. The position of La Braña individuals in the 1000 Genomes Project data and the 1KG Pomnichip PCAs suggests that the uniform Mesolithic substrate could be related to modern Northern European populations but may represent a gene pool that is no longer present in contemporary Southern European populations. In the latter PCA, where the origin of each Iberian sample is known, it is possible to see that the Mesolithic specimens are not related to modern Basques, contrary to what has been previously suggested in some recent studies [39].

Ancient genomics from Neolithic individuals from Scandinavia [18] supports that the spread of agriculture into Europe involved the expansion of populations from the Middle East that eventually assimilated the contemporaneous hunter gatherers. Modern European populations seem to derive essentially from those Neolithic migrants [18]. Until now, however, the genetic affinities of the Mesolithic populations to the modern Europeans were largely unknown. Our partial La Braña 1 and 2 genomic data show that modern Iberian populations are not descendants of the local hunter-gatherers inhabiting the same region prior to the arrival of farmers and thus support a genetic shift in that region between the Mesolithic and modern populations.

In figure-S2, one can see that the Mesolithic Individuals are Asian-shifted with respect to modern Europeans.

The in figure-S3, one can see that the Mesolithic Individuals cluster within NW Europeans, that is CEU and GBR, now Basques appear to be as distant from them as Finns are, so it is not a Northern vs. Southern European thing, but NW Europeans having the closest similarities and then Southern Europeans and Finns. Granted some Finns do cluster very close to the individuals, whereas the closest Iberian individual is not even a Basque, but someone from Valencia.

From an archaeological point of view, I find this believable. The main expansion post-LGM was in the Magdalenian culture which is now thought to be an intrusion from the east about 18000 years ago. They then spread out all over west, central and northern Europe in various guises. I suspect this uniformity is due to most hunter-gatherers having common roots about 20000 years back in the east meaning there was little deeper time east-west refuge contrast that contributed to modern DNA.

This could have some support on the fact that the two hunter-gatherers do seem to be Asian-shifted in Figure-S2. However, they are definitely post-Magdalenian, as their dating is 7000 ybp, clearly outside of the Magdalenian period.

This is another blow to any notion that the Basques were in-situ descendants of an ice age western refuge. Most already thought this in terms of yDNA and now mtDNA and autosomal is strongly agreeing with this. It is of course a tiny sample.

From the autosomal* point of view, yes, there is definitely some re-thinking to do, given that Basques aren’t any closer to these Mesolithic Iberians than other Iberians. From the yDNA point of view, well British guys who are majority R1b are the closest modern Europeans to these Mesolithic samples, from the mtDNA point of view, there is evidence that points to the presence of mt-DNA H in Magdalenian Cantabria, and mt-DNA H in Mesolithic Guipuzcoans.

*Now that I think of it, they said the following in the abstract

Quote from: Sanchez.Quinto.et.al.2012

Furthermore, analyses of 1.34% and 0.53% of their nuclear genomes, containing about 50,000 and 20,000 ancestry informative SNPs, respectively, show that these two Mesolithic individuals are not related to current populations from either the Iberian Peninsula or Southern Europe.

But in Figure-S3 we do find the Iberians to be closely related to the two folks:

As a whole they are indeed closer than Finns, although not as close as NW Europeans. Something else I noticed in PCA plot S3, is that Basque usually cluster in a certain location tightly relative to the other Iberians, however here they are scattered all over the place, this might be due to the smaller number of SNPs used to construct the plots.(50,000 and 20,000 SNPs respectively)

This means that they did sequence the y-chromosome, too bad they didn't release the haplogroups.

Although this is long post-Magdalenian, its usually thought most western, north-west and central European late Upper Palaeolithic has Magdalenian ultimately. From memory in Iberia and adjacent it first transformed into the Azilian. It doesnt surprise me that the genes of these hunters survives strongest in Britain etc. It also doesnt surprise me that Iberians are not closely related as I understand that after the Azilian Iberia a lot of the Iberian hunting population is through to have disappeared except in a few area.

In terms of closeness it goes roughly NW Europeans>Western Scandinavians/Germans>Iberians>North Italians>Eastern Europeans>NorthEastern Europeans>Greeks and South Italians.

It is noteworthy that Northeastern Europeans such as Lithuanians, Finns, Russians are very distantly related to this Hunter Gatherers, contrary to the recent popular beliefs amongst some that the Iberian HG would look very Baltic, they don't. This could mean that NE Europeans descend from other Mesolithic Europeans, who were not similar to the Iberian HG.

Dienekes has just posted a really interesting summary. Very compelling in its simplicity. I notice that the Atlantic-Baltic vs south divide makes a lot more sense than when it is split into Northern and Atlantic -Med. The first system shows a very straight forward Meso-farmer divide. When you split it into Northern and Atlantic-Med. it removes the nice simple divide because it makes both hunters and farmers Atlantic-Med in part. However the fact the Iberian hunters are about half and half northern and Atlantic-Med shows that Atlantic-Med was pre-farming too. The main difference then is the 2nd system seems to make a lot more farmers blood pre-farming whereas the simple Atlantic-Baltic vs southern gives a much more clean division.

Anyway Dienekes paints a very compelling picture of three main strands in the DNA - hunters (with a northern stronghold attested early), farmers (with a SE to NW cline and attested from the inception of the Neolithic) and what he calls a SW Asian stain (not attested yet in the pre 3000BC samples). He sees the latter as likely the IE strand (it is missing among Basques and Sardinians) and he seems to be suggesting an origin among the mountain fringes of SW Asia, kind of in the fringe between the early farming and the steppe zone. He obviously realises that the shape and the presence or lack of it in Neolithic populations means it cant be places in the main highways west of early farming so he has pushed it a little north without quite embracing the Kurgan model. I think the challenge now is whether SW Asian is a good term or are the highlands of SW Asia just a kind of a refuge zone.

In terms of closeness it goes roughly NW Europeans>Western Scandinavians/Germans>Iberians>North Italians>Eastern Europeans>NorthEastern Europeans>Greeks and South Italians.

It is noteworthy that Northeastern Europeans such as Lithuanians, Finns, Russians are very distantly related to this Hunter Gatherers, contrary to the recent popular beliefs amongst some that the Iberian HG would look very Baltic, they don't. This could mean that NE Europeans descend from other Mesolithic Europeans, who were not similar to the Iberian HG.

Well that would not be hugely surprising to me anyway. I recall that the basic repopulating of Europe after the ice age is seen as coming from two directions, the Magdalenian and its derived cultures and another group of cultures coming from the Ukraine sort of direction with both overlapping to some degree in northern Europe but perhaps with the extreme NE fringes of northern Europe getting a lot less from the western refuge. They were ultimately related 20000 years back but separated then for a hell of a long time. You can see why people wrongly linked this to R1b and R1a years back. However, even with that correlation gone, these movements still happened even if not well reflected in the yDNA. Interestingly when the Atlantic-Baltic group is split into northern and Atlantic Med, the Iberian hunters were about 50-50 of both. That doesnt make sense to me so I have my doubts about the latter clustering.

Dienekes has just posted a really interesting summary. Very compelling in its simplicity.

Far too simple to compel me, but interesting I grant you. Whatever his West Asian component is, it can't be a major IE strand if there is more of it in Greeks than Slavs and Germanic speakers. Greeks are notably low in the major Y-DNA haplogroups that are well known to correlate with IE speakers. In fact they are a stand out exception, seeming to have assimilated much more in the way of previous Neolithic people. Nor can it have much to do with IE speakers if it is strong in the Caucasus.

One big problem for his analysis is that IE speakers arose from mesolithic hunter-gatherers carrying mtDNA U5 and U4, just like the people of the rest of Europe in the Mesolithic. Yes they mixed with dairy farmers of an Anatolian origin, but his massive supposedly Mesolithic component is liable to have actually arrived in most places in Europe in the Copper Age.